FWIW I don't think this is a real issue. It is right now because Lemmy is fairly new and small. But over time it will become obvious which communities are popular and people will go there. I think there is a small issue because local communities are sort of given priority as /communities defaults to "Local". But that sort of seems like the end of the list.
Just like it isn't an issue that people can create "Cats" and "CuteCats" on Reddit I don't think it is an issue that you can create cats@a.example and cats@b.example. Over time people will find and participate in whichever popular community matches their preferences.
I don't like the idea of global "Multi-communities" as now there are more instance admins that have control over a community. I think that in general mods should have the most control, instance admins being necessary due to an implementation detail (communities are bound to servers) and should only need to step in for extreme cases. (Like violating server rules)
I don't mind "Communities following communities" as much but I fail to see the point. If you think that another community is a good place to have a discussion why not just tell your members that you recommend moving there? I can see this working as a "Public Playlist" style idea where you can subscribe to follow recommended communities. I think having the option to post to both a followed community or the community that is doing the following is unnecessarily confusing. Basically I would make this as more of a discovery feature than a way to merge communities together.